upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test> trac-all -prep -c /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example.txt
INFO: SUBJECTS_DIR is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/dmrirc.local -log /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/trac-all.log -cmd /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Wed Oct 27 13:41:01 CEST 2021
rm -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs
mri_convert --bvec-voxel /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz
mri_convert --bvec-voxel /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz 
reading from /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm...
Getting Series No 
INFO: Found 125 files in /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI
INFO: Scanning for Series Number 27
Scanning Directory 
INFO: found 123 files in series
INFO: loading series header info.

RunNo = 26
WARNING: Run 1 appears to be truncated
  Files Found: 123, Files Expected (lRep+1): 1
FileName 		/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32875290.dcm
Identification
	NumarisVer        syngo MR E11
	ScannerModel      Prisma_fit
	PatientName       ANONYMOUS 
Date and time
	StudyDate         20190410
	StudyTime         080641.596000 
	SeriesTime        090254.994000 
	AcqTime           090128.605000 
Acquisition parameters
	PulseSeq          *ep_b0
	Protocol          DQS_SCAN
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          82
	InversionTime     -1
	RepetitionTime    4400
	PhEncFOV          211
	ReadoutFOV        211
Image information
	RunNo             26
	SeriesNo          27
	ImageNo           1
	NImageRows        768
	NImageCols        768
	NFrames           123
	SliceArraylSize   64
	IsMosaic          1
	ImgPos            903.8222 801.9736 -66.6789 
	VolRes              2.1979   2.1979   2.2000 
	VolDim             96       96       64 
	Vc                 -0.9973   0.0723   0.0120 
	Vr                 -0.0715  -0.9958   0.0566 
	Vs                  0.0160   0.0556   0.9983 
	VolCenter           0.0000   0.0000   0.0000 
	TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: ( 96  96  64), nframes = 123, ismosaic=1
sdfi->UseSliceScaleFactor 0
INFO: rescale not needed
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR E11
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 4400, TR = 4400 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 1.00000   0.00000   0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;

FileName 		/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32875290.dcm
Identification
	NumarisVer        syngo MR E11
	ScannerModel      Prisma_fit
	PatientName       ANONYMOUS 
Date and time
	StudyDate         20190410
	StudyTime         080641.596000 
	SeriesTime        090254.994000 
	AcqTime           090128.605000 
Acquisition parameters
	PulseSeq          *ep_b0
	Protocol          DQS_SCAN
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          82
	InversionTime     -1
	RepetitionTime    4400
	PhEncFOV          211
	ReadoutFOV        211
Image information
	RunNo             26
	SeriesNo          27
	ImageNo           1
	NImageRows        768
	NImageCols        768
	NFrames           123
	SliceArraylSize   64
	IsMosaic          1
	ImgPos            114.5128 119.9261 -16.0192 
	VolRes              2.1979   2.1979   2.2000 
	VolDim             96       96       64 
	Vc                 -0.9973   0.0723   0.0120 
	Vr                 -0.0715  -0.9958   0.0566 
	Vs                  0.0160   0.0556   0.9983 
	VolCenter           2.8832  26.4046  61.5000 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = 0.0160358 0.0555939 0.998325
INFO: no Siemens slice order reversal detected (good!). 
TR=4400.00, TE=82.00, TI=-1.00, flip angle=90.00
i_ras = (-0.997313, 0.0722762, 0.0119947)
j_ras = (-0.0714883, -0.995834, 0.0566035)
k_ras = (0.0160358, 0.0555939, 0.998325)
writing to /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz...
Saving bvals and bvecs
mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.voxel_space.bvecs /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs
mri_probedicom --i /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm >> /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dcminfo.dat
rm -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals.tmp /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs.tmp
mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs.tmp /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs
mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals.tmp /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals
orientLAS /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 10.6278
mri_convert -oni 96 -onj 96 -onk 64 -oid -0.997313 0.0722762 0.0119947 -ojd 0.0714883 0.995834 -0.0566035 -okd 0.0160358 0.0555939 0.998325 -oc 3.04032 28.5934 61.3756 -rt nearest /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz
mri_convert -oni 96 -onj 96 -onk 64 -oid -0.997313 0.0722762 0.0119947 -ojd 0.0714883 0.995834 -0.0566035 -okd 0.0160358 0.0555939 0.998325 -oc 3.04032 28.5934 61.3756 -rt nearest /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz 
normalizing out_i_direction: (-0.997313, 0.0722762, 0.0119947) -> (-0.997313, 0.0722762, 0.0119947)
normalizing out_j_direction: (0.0714883, 0.995834, -0.0566035) -> (0.0714883, 0.995834, -0.0566035)
normalizing out_k_direction: (0.0160358, 0.0555939, 0.998325) -> (0.0160358, 0.0555939, 0.998325)
reading from /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz...
TR=4400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997313, 0.0722762, 0.0119947)
j_ras = (-0.0714883, -0.995834, 0.0566035)
k_ras = (0.0160358, 0.0555939, 0.998325)
Reslicing using nearest 
writing to /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz...
INFO: found /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals, copying
INFO: found /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs, converting to LAS
mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvecs /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs
mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
mri_convert --frame 0 /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las.nii.gz
mri_convert --frame 0 /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las.nii.gz 
reading from /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz...
TR=4400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997313, 0.0722762, 0.0119947)
j_ras = (0.0714883, 0.995834, -0.0566035)
k_ras = (0.0160358, 0.0555939, 0.998325)
keeping frame 0
writing to /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las.nii.gz...
bet /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain.nii.gz -m -f 0.3
awk: fatal: cannot open file `/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory)
eddy_openmp --imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz --mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs --bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals --acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt --index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt --data_is_shelled --out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi
EddyInputError:  Error when attempting to read --index file /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
Terminating program
Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18 20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021

upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>